Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.10.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07815	0.947
27DAP/17DAP	1.17475	0.849
39DAP/27DAP	1.00397	0.857
41DAP/39DAP	1.40845	0.468
42DAP/41DAP	0.63062	0.774
43DAP/42DAP	1.01995	0.937
47DAP/43DAP	1.17697	0.278
52DAP/47DAP	0.88887	0.673
57DAP/52DAP	1.00041	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.8465	0.046
17DAP/reference	0.90328	0.085
27DAP/reference	0.96867	0.61
39DAP/reference	0.93726	0.424
41DAP/reference	0.89385	0.267
42DAP/reference	0.84221	0.037
43DAP/reference	0.96623	0.611
47DAP/reference	0.84995	0.05
52DAP/reference	0.838	0.108
57DAP/reference	0.89645	0.221

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28334	0.372
27DAP/17DAP	0.8468	0.748
39DAP/27DAP	1.23179	0.526
41DAP/39DAP	1.26011	0.565
42DAP/41DAP	1.34253	0.708
43DAP/42DAP	0.80736	0.216
47DAP/43DAP	1.29807	0.033
52DAP/47DAP	1.61663	0.173
57DAP/52DAP	1.41761	0.523
57DAP/7DAP	1.73258	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01155	0.758
17DAP/reference	1.12717	0.754
27DAP/reference	1.02738	1
39DAP/reference	0.79027	0.083
41DAP/reference	0.6898	0.011
42DAP/reference	0.77818	0.018
43DAP/reference	0.95591	0.421
47DAP/reference	0.87683	0.222
52DAP/reference	0.99634	0.679
57DAP/reference	1.12028	0.438

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91712	0.426
17DAP/reference	0.96011	0.474
27DAP/reference	0.78343	0.15
39DAP/reference	0.87319	0.195
41DAP/reference	0.89088	0.212
42DAP/reference	0.87402	0.169
43DAP/reference	1.07924	0.919
47DAP/reference	0.88095	0.083
52DAP/reference	1.00116	0.666
57DAP/reference	0.96403	0.549

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08123	1
17DAP/reference	1.06058	0.775
27DAP/reference	1.14508	0.115
39DAP/reference	0.90288	0.111
41DAP/reference	1.1557	0.383
42DAP/reference	0.9894	0.816
43DAP/reference	0.84715	0.143
47DAP/reference	1.00334	0.708
52DAP/reference	2.66637	0.118
57DAP/reference	0.9171	0.315

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.31071	0.966
26DAP/20DAP	0.83941	1
34DAP/26DAP	1.3418	0.542
51DAP/34DAP	1.12787	0.565
52DAP/51DAP	0.95159
53DAP/52DAP	0.87932	0.663
55DAP/53DAP	1.32747	0.048
57DAP/55DAP	0.68696	0.058
62DAP/57DAP	0.86306	0.466
68DAP/62DAP	1.48828	0.066
68DAP/14DAP	0.97672	1

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.5893	0.079

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	2.31372	0.363
Immature Eggplant/Mature Eggplant	1.18536
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	2.71225

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	0.93348
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.05309	1
IL2-6/WTpooled	0.7503	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.08974	1
IL12-4/WTpooled	1.05446	0.839
IL1-4/WTpooled	1.06378	1
WT/WTpooled	0.9862	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.9031	0.975

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04146
DC3000/delta hrp 6h	0.91308	0.95
DC3000/delta hrp 12h	1.0725	1
DC3000/delta hrp 24h	0.98782	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.30977
DC3000 delta B/DC3000 delta AB	1.14917	0.462

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.09849	1
Exp 36h	N/A	N/A
Exp 60h	0.91308	0.855

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.98285	1
Var 0h	0.96033	1
Var 12h I row2-row1	0.86347	0.353
Var 12h NI row2-row1	1.00288	1
Var 36h I row2-row1	0.98344	1
Var 36h NI row2-row1	1.27941	0.253
Var 60h I row2-row1	0.87059	0.374
Var 60h NI row2-row1	1.22518	0.904
Time course 0hI-0hNI	1.12214	0.833
Time course 12hI-12hNI	0.90867	0.248
Time course 36hI-36hNI	0.84825	0.023
Time course 60hI-60hNI	0.60174	0.009

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.10079	0.431
transgenic ySAMdc/azygous control (breaker)	1.15499	0.248
transgenic ySAMdc/azygous control (red)	1.1037	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05938	0.125

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98962	0.789

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95973	1
Manapal/WT (break)	0.95362	1
Manapal/WT (red)	1.16375	0.222